


Pokemon Ninja

by YukimorioftheCherokee



Category: Naruto, Pocket Monsters: Omega Ruby & Alpha Sapphire | Pokemon Omega Ruby & Alpha Sapphire Versions
Genre: Revived Shinobi
Language: English
Status: In-Progress
Published: 2020-12-12
Updated: 2020-12-11
Packaged: 2021-03-11 04:28:34
Rating: Teen And Up Audiences
Warnings: Creator Chose Not To Use Archive Warnings
Chapters: 1
Words: 5,147
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/28019274
Author URL: https://archiveofourown.org/users/YukimorioftheCherokee/pseuds/YukimorioftheCherokee
Relationships: idk
Kudos: 1





	Pokemon Ninja

Pokemon Ninja

# Chapter 01: Rebirth

The eleven year old Uzumaki Naruto wakes with a gasp. The boy, believe it or not, is staring at the sky from where he lays in a small hammock. The boy, somehow, remembers growing old and is now awake here. Sitting up, he glances around, using his heightened senses to try and figure out where he is at. He pauses when he hears someone calling for help. Naruto leaps to the ground before rushing around a corner to find a canine creature attacking an older fellow. 

“Professor Birch!” A kid calls as she starts to reach for the bag on the ground. 

Knowing from the man’s instructions that something useful is within Naruto ignores the cute girl before he leaps into the air, using a drop kick to form a crater between the canine and the professor. The dog yelps before it darts off into the taller grass, hiding from his sight. “Uh, how did you make a crater?” The girl asks. Her head is tilted toward the left and the professor is analyzing him with his gaze alone. 

Naruto shrugs, not seeing it useful in telling any of his secrets before the professor sighs. “Well, you both came to rescue me, so how about I give you both a pokemon. Pick one out of the bag.” The girl’s eyes sparkle as she reaches into the bag. Three red and white balls are pulled out and she tosses one ball to see what is inside it. 

Naruto watches an energy source similar to that of the Biju exit the ball, forming a red chick that Naruto senses has a fire affinity. The red chick chirps at her, with glittering eyes. “Yay! She chose me!” 

“Not this one.” The bird chirps sadly. Naruto takes the ball before she can put the bird back into it before he lifts it onto his shoulder. The bird chirps, confused for some reason before the girl cries, “Yes, Mudkip!” The mudkip is looking at her skeptically at the childishness she has shown in discarding the bird so easily. 

“Do you have a name?” Naruto asks his bird. 

“Call me Rubedo, and I am male in case you can’t tell.” Naruto pets his beak before the Professor clears his throat. 

Naruto looks up at the man, seeing a curious gaze in his eyes. “You understand pokemon?” He asks, literally waiting for the answer with bated breath. 

Naruto snorts, now knowing that these creatures are called that. Before he can answer the girl makes a noise of conclusion. “I’m naming my Mudkip Kipper.” Kipper smiles at her, not completely satisfied but still agreeing. 

Naruto turns his attention toward the nearby town they have come from. “No, but if you learn how to read body language, animal traits and other things you can get a generic understanding. Might not be perfect, but from my understanding mine’s name has something to do with rubies… Is it Rubedo?” Rubedo chirps shrilly, nuzzling his cheek quite happily. Naruto chuckles as he sees that Rubedo has nearly fallen off his perch and the bird gives him a somewhat upset look.

“I thought it was cute.” Naruto answers the unasked question easily enough before the bird blushes, which doesn’t seem easy with how it has feathers covering it. 

Rubedo leaps off his shoulder, landing on the ground before he chirps at him. “Where to boss?” Naruto turns toward the professor and gives him a small smile. 

“Professor, do you need an escort back to town?” Naruto asks him with some worry. The professor clears his throat like it is a troubling thought. 

“I can help you too, Professor Birch!” Birch gives them smiles, with his gaze softening as he looks between them. 

“Actually, I can make my way back on my own. Though, if you want to, you can train your pokemon nearby before coming back to me for an extra reward later. Maybe even have a battle between the both of you once you reach the water’s edge of Route 103.” The girl grins happily. 

“Sure thing professor, my Dad’s a Gym Leader, I’ll win as there will be no contest!” Naruto raises an eyebrow, realizing that people battle using the pokemon instead of fighting themselves. 

“Give me a little while to train up and we’ll see.” Rubedo chirps in a way that reminds Naruto of cackling before Kipper bristles. 

“Sure, but mine is a water type, yours is fire. Who do you honestly believe is going to win?” She asks with honest curiosity. Naruto snorts at her, knowing that thought has been prevalent in his past life. 

“Just because Rubedo’s type is weak against Kipper’s doesn’t mean that Rubedo won’t win. I have no doubt that I can train Rubedo enough to beat the first gym leader on his own. Doesn’t mean I have to put all the pressure on him like that but I’m confident that it can be done.” Rubedo lunges, nuzzling the side of his leg with tearful joy as he tries showing his appreciation. Naruto picks him up, holding him gently as the bird cries at having someone be so confident in his abilities. 

The girl stands up taller, and the Professor seems to be quite curious as to how this can work out. “Well, I’m May, and I’m challenging your words. I bet that he can’t win by himself! And this means you can only use Rubedo in your fight against the Rock Gym Leader, Roxanne!” Naruto snorts at her, knowing that it may be something he is willing to test. 

“I bet all my healing supplies I have after the gym battle. How about you, what are you betting?” May pauses, not knowing what to think before she smirks. 

“I’m sure that you can bet half of your medical supplies and match him, May.” Professor Birch tells her earning a firm nod from May. 

“Deal?” She asks Naruto, he nods to her, knowing that he can train Rubedo up faster than she can. 

“Professor Birch, care to visit the Gym when I go to battle Roxanne? Just as a witness so May doesn’t get the idea that she can back out?” Naruto asks him, earning a firm nod and a smile from him. 

“Why this is an unusual challenge, I’ll be letting Roxanne know to eventually expect you so I can come watch. I’ll even send for Norman, May’s Gym Leader Father.” Naruto smiles at him, nodding once, before he turns toward the road and clicks his tongue. Rubedo falls into step behind him, surprising May that he is headed straight for the tall grass. 

“Well, looks like we have quite the challenger.” Brandon says as he appears, having come from the town that the professor is now headed toward. 

“It certainly seems so.” He says with one glance at May, who seems more interested in doting on her new Pokemon than preparing for the battle. 

* * *

Naruto sighs, seeing that Rubedo is tired from fighting nearly thirty pokemon, one after another. Naruto scoops him up into his arms and heads toward the next town, seeing something resembling a hospital from this close to the town’s edge. As soon as he comes into sight of the hospital doors a man wearing a blue apron walks up to him smiling at him. 

“Hi there, I work at the PokeMart.” He offers his hand for a shake, which causes Naruto to have to tuck Rubedo against his side to hold him while being able to shake his hand. “From what I can see, you’re a novice trainer. Am I right?” He smiles at him when Naruto blushes at having been caught with his pokemon a little too exhausted. “Ok. Being super kind hearted as I am, I’m going to give you some useful advice.”

Naruto watches him point out the building in the square with the blue roof. “First of all, that’s a PokeMart there. Just look for our blue roof. We sell a variety of goods, including pokeballs for catching pokemon!” Naruto startles when he pulls out small bottles. “I’d like for you to have these as a part of a special promotion! They are potions, spray it onto any wounds and they will heal up almost instantly. Potions can be used anytime, so they can be very useful to have.”

The pokemart clerk motions toward the red roofed hospital. “And that is a Pokemon Center! Look for a red roof! Ask a woman inside and she will restore your pokemon’s health. That’s all the advice I have. Have a great journey!” The man turns toward the blue building and goes toward it as Naruto watches him curiously. He pockets ten potions. He chuckles a little, wondering if there is a way to make his own potions. 

Naruto heads inside the Pokemon Center and walks up to the counter where the nurse is waiting. She is obviously the person that the clerk wanted him to ask or she wouldn’t be behind the desk with the medical machines. “Hey, I need Rubedo to be healed.” Naruto tells her as he gently puts his partner on the counter. 

“Okay, I need him inside his pokeball.” He pulls out the pokeball and watches Rubedo willingly return into it before the nurse gently takes Rubedo’s ball from him. She puts it on the machine and he watches an image of Rubedo appear behind the desk on the monitor. The pokeball glows a few times, covered by green healing chakra, before it stops and the nurse hands him back to him. “I’m one of the Nurse Joy Family. We all go into the nurse business and enjoy healing up wounded pokemon. If you need a place to stay we have a few rooms upstairs.” 

Naruto shakes his head at her offer. “That is mighty kind of you, but we are training to take on Roxanne. I took on a bet that Rubedo can defeat her pokemon by himself so I’m going to be training him like crazy. He is already twice the strength that he was when I met him.” Naruto takes Rubedo’s ball and releases him to allow him to follow after him. Before Naruto can react Rubedo steals a treat from Nurse Joy’s pocket and Naruto smiles as he hears her giggle happily. She pets Rubedo’s beak, like he did earlier, and she coos at him. 

“I guess we could use a meal before we go anywhere.” Naruto says before she nods to him. Naruto takes Rubedo from her and briefly pauses as he realizes that he does want to keep a few things secret. “Now that I think about it, is it allowable to come here and use a room to eat privately in? I’m hopeful that I have pencil and paper to take some notes.” Naruto turns toward his kunai pouch, barely realizing that he also has a medical pouch and a backpack. 

“Of course, it is always smart to plan your trips out to experience the full joy of being a trainer!” Nurse joy tells him happily. Naruto smiles at her before another nurse, identical to the first, comes out of the back. 

“I’ll be happy to guide you to a private room. These rooms are free to trainers traveling. However, we ask that you keep it down since this is a hospital for pokemon. There are exhausted trainers resting in them more often than not. So please try to be respectful of others and their need for rest.” Naruto smiles at her, nodding his head in agreement. This time he isn’t stuck here so he doesn’t honestly mind. 

“Yes, Ma’am. I’ll keep it quiet so as to not disturb the rest of the patients. Do you happen to know where I can find information on crafting pokeballs?” Naruto asks Nurse Joy before she frowns at him. 

“That is a highly dangerous task. It requires ancient writing to be used with an apricorn and can literally explode in your face if you aren’t careful.” She tells him cautiously and Naruto sees that she is hesitant to share it with him. 

“I’m planning on trying to make my own pokemon storage system, and am wondering if the uses of pokeballs can be combined to create a temporal space where Pokemon can relax when not being called upon.” Naruto tells her earning wide eyes that instantly start giving him shrewd looks. 

“Who taught you?” Naruto blushes at his discovery of it being possible. 

“I have been doing self research ever since finding my ancestor’s notes, he was Jiraiya of the Sannin.” Her eyes widen drastically before she nearly faints. Naruto gently guides her to a chair in the hall that they are now in and she looks up at him. 

“His findings were supposedly lost along with that of Naruto.” Naruto blushes at the news. 

“Yeah, I changed my name to Naruto recently, Uzumaki Naruto.” She smiles at him softly. 

“That is going to be really difficult to raise to their levels. Naruto sealed a giant Ninetails into himself, making him be a human pokeball. After that a few people started trying to decipher the writings to make their own way of carrying their pokemon. Back then, though, they were called animals.” Naruto nods to her, knowing that she is being honest with him. 

“Yeah, but they are generally called seals and the art of making seals is Fuinjutsu. Apparently every town and village used to be full of ninja back then.” Nurse Joy blushes before she looks at him suspiciously all of a sudden. 

“I suppose it would be rather interesting to see if you can decipher the seals.” Naruto chuckles, knowing that she suspects him of being the actual Naruto Uzumaki. With Kurama not saying anything he doubts that any of the Biju are sealed inside of him. 

“How about I go to a room and wait for you to bring it to me. I’d be glad to see if it is anything similar to the Fuinjutsu I learned. I have this one right here.” He pulls his storage scroll out before unsealing notebook papers with fuinjutsu notes. She gently leans over to look at the pages, before she frowns. 

“This seems brand new compared to the original notebooks.” She says with awe and confusion. 

“I managed to use a seal to copy the writing, word for word, into a notebook. I was sure that I would damage the original works if I carried them around with me.” He answers her easily enough. She smiles at him before she stands and guides him and Rubedo down the hall a little further. She suddenly stops and opens a door, and Naruto peers inside to find a very nice room complete with a computer desk. 

“Now usually we don’t have people in this room because it is meant for researchers, but if you don’t steal any information or use it against the Police, the Pokemarts or the poke Centers then I will allow you to look up a few different things. But do withhold from outright stealing Professor Birch’s information from the computer.” Naruto frowns before an idea comes to him. 

“Nurse Joy, would it be alright if I set up a contract to work with the various Pokemon Centers as a researcher and a Fuinjutsu expert?” She pauses for several moments before she nods to him. 

“I’ll ask Professor Birch to preside over the interview.” Naruto smiles at her. 

“I did not expect that I would see him so soon after getting Rubedo from him.” Rubedo quickly makes a beeline for the water and food bowls set aside for him. 

“Oh, you’ve already met?” She asks him and, before he can answer she chuckles. “That makes things a little easier.” Naruto clears his throat, causing her to look at him attentively. 

“I promise not to misuse the information in your database. Otherwise I won’t go snooping where I’m not needed. Though I would ask if looking up pokemon elemental weaknesses and strengths count as going too far. I could make a chart.” She giggles at him. 

“I guess that you paid more attention to fuinjutsu than class studies. I’ll be happy to find a type chart from behind the desk for you to have as a reference.” She says happily. 

“Yeah, sorry.” She waves her hand. “The password is Catching103 since that is the class he taught when in charge of the regional college.” Naruto nods to her as he turns toward the desk. Seeing that it has Birch’s name as the username he types in the password and watches the network activate. 

“Are you sure you should have told her that?” Rubedo asks. 

“I’m sure. When I prove myself they will understand.” Rubedo relaxes before going back to feeding and Naruto feels his intelligence being tested by most of the gibberish until he decides to use the search bar. Instantly, he finds apricorn balls and opens the ball’s writing. A 3D image of the inside of the ball appears and Naruto takes a moment to read it. He sweat drops at how simple it is, yet the others claim that it is difficult to do according to the notes on the bottom. 

“Seriously? This is way too easy to understand the array yet they call it difficult. Bah, they’ve never been challenged before!” A whistle comes from outside the door and Naruto looks up at professor Birch, realizing that he has been making notes in the back end of his notebook on the different arrays. 

“Look at the other ball’s arrays. Each Apricorn Ball is made with a different seal.” Naruto makes a notation of such on his first ball, and the type that it is, before he goes to the next page. Naruto ends up taking notes for a little while.

* * *

Naruto grins at having deciphered the pokeball machinations. “Whoa, I never knew anyone who could disassemble it so fast.” Birch says, awed by his work. 

“You wouldn’t happen to have an extra pokeball, would you?” Professor Birch hands him a pokeball and Naruto opens it, studying the seal inside of it and writing notes on it as well. 

“This is amazing, this is supposed to be one of the hardest things to create yet you created another by accident on the paper.” Naruto looks at the alternate seal he wrote down for the water type, seeing it glowing for several moments before it makes a clicking noise. Naruto pushes his chakra into the centerpiece before a bird pops out. “Whoa! You made a Healing ball! We’ve yet to discover a working method of healing pokemon after they are caught so this is going to be legendary.” Naruto blushes at the praise before he takes a moment to look at it. Naruto burns the paper, freeing the angry bird before it blinks at him. 

“I’m not going to force you to be one of my partners. I wouldn’t want to be forced into anything and so that is how I will treat all pokemon.” The bird squawks at the news in surprise before it decides to observe him instead. 

“I’ll go get a few apricorns for you to make them!” Professor Birch says before Naruto sighs and turns toward the confused Rubedo. 

“I guess we have a way to make a living now, don’t we?” Rubedo nods to him firmly with a happy chirp. Naruto sighs before looking outside the window. It is dark outside so he sighs. 

“Looks like it is time for a shower and bed.” Naruto says before Rubedo gleefully rushes toward the shower. Naruto follows after him and blinks when professor Birch enters the other door and looks around for him. 

“I’ll work on it tonight, but I ask that all the cameras be turned off.” Professor birch nods to him with a broad smile before he drops the three boxes of apricorns on the desk. Two Nurses follow after him, bringing two boxes each. “I’ll easily get them done before morning.” Naruto tells them before going inside to take a shower. He closes the bathroom door behind him as they lock the bedroom door behind them to give him privacy that he has asked for. 

* * *

Naruto stretches the next morning, glancing around the room to find many more pokeballs than he had accounted for the night before. Three clones are still working on the different balls before Naruto gets up, snatches his breakfast up, and begins eating it hungrily. He forgot to eat last night and he feels silly for it. 

A knock sounds from the door and Naruto watches his clones put the last touches on the balls and vanish in puffs of smoke. “Come in!” He says, glad that he slept in actual Pajamas this time instead of only his boxers. Professor Birch enters the room with a police officer behind him. 

“May I call you Naruto?” The officer asks him and Naruto knows that they noticed. 

“If this is about the lack of records then blame team rocket. They tried keeping me under wraps for a long time but thankfully I managed to escape.” The officer’s eyes are wide and she sighs, almost like she is reluctant to leave him on his own. 

“Well that’s horrible! I bet they were up to something nasty. They tend to steal pokemon and if you could make a pokeball that steals pokemon from other pokeballs then that would be catastrophic!” Professor Birch exclaims in a near panic. 

“I didn’t share anything with them.” Naruto lifts his shirt up and they stare at his numerous scars. “I refused to so they took to torturing me, though they never thought to take the seals stuff out.” Naruto says before he takes another bite and the officer takes a moment to write down her observations. “So I managed to attach bomb seals to the Apricorns they wanted me to use.” Birch startles at the news. 

“Bomb seals?” Naruto snorts at him. 

“They were then used to escape and I doubt that Team Rocket would have told anyone about me. They knew that my scroll is keyed to my lifeforce. They called it aura but it is actually called chakra.” Birch startles at the news. 

“So that is how you managed to make the crater near Littleroot Town.” Naruto nods to them. 

“I managed to get the aura suppression cuffs off of me before I went out of the room as well. Since they are also made with seals it was easy to use the counter seal for it. Then I managed to break the cuff and crumbled it to pieces so they couldn’t steal my work.” Naruto slowly starts to realize that he isn’t lying, that he actually has memories of fighting to get out. 

“They used the Pokemon Cloner to recreate me. I really am Naruto, and I have all his knowledge and memories, but they didn’t account for everything being there. They also amplified my Chakra and caused it to be chaotic when used. Since then I’ve not been using it as much due to how destructive it is.” Naruto remembers how his chakra is definitely more controllable than it was half way through his training, but without an actual tutor he might actually do something horrible. He remembers actually killing a few pokemon when they went to test his power. He also stole all their DNA Results from the tests used to clone his former friends. He sadly left them a message in plain sight of their containment areas, hoping they will believe him. 

“I apologize, but we need to know where it is.” Naruto looks at the officer and stares her down. 

“No. I’m not returning there. All you need to know is to look for it in the ocean south of here, through the forest surrounding Littleroot Town and even further south from there. They have disguised it so I doubt that you will find anything of use to help track them. They were cloning the original Naruto’s friends as well. I left messages in the ancient language we used for them to read.” The officer nods before she turns toward Professor Birch. 

“I’ll leave him in your hands for now.” He sighs before Naruto realizes that Birch doesn’t want to hold him back. 

“How often do I have to call you?” BIrch blinks, not having expected it. 

“Once a week minimum.” Birch tells him after thinking it over. “Please don’t do anything reckless like you did in your other life.” Naruto smiles, nodding to him briefly. 

“In that life I hated studying. In this life they taught me how to read, write and speak your language since I made temporary clones that would teach me what they learned when I dispel them. Watch.” Naruto focuses a little chakra before five copies appear and Nurse Joy is giving him a stern look. 

“So you made your clones do the writing? I wish I had an ability like that.” Naruto remains quiet despite knowing that he can teach her how to access it. 

“The world is not ready to remember the bloody past it once has been filled with.” Nurse joy calms, realizing that such power will and can kill others. 

“I understand. Since you are now a ward of Professor Birch I can easily set up your own account here at the Pokemon Center.” Naruto nods to her, knowing that he will be able to brighten the future here instead of remaining in the past. 

* * *

Naruto heads north to the edge of the water on route 103 since he has been training some more. He also has prepared to face May and her pokemon. He wonders if she has any extra pokemon before he sees her. She is gathering information on different pokemon and he walks up to her, peering over her shoulder at the pokedex she now has. “Hi, May.” She squeals as she whirls toward him before she grins victorious. 

“Get ready to be squashed like a bug.” She declares bravely. 

She tosses out Kipper and Naruto grins. “Rubedo, scratch!” Rubedo leaps into the air before landing with claws racking down Kipper’s side. 

“Tackle!” Kipper rushes at Rubedo who takes the full brunt of the attack. 

“You call that tough, ha! My Granny has a more powerful scratch than that!” Rubedo chirps aggressively. Kipper glares at him. 

“Scratch again.” The repeated attack has Kipper looking bad and May seems nervous. 

“Kipper, Growl!” Kipper growls really cutely and Naruto hears Rubedo. 

“Aw, how cute.” He murmurs and Naruto realizes that it is similar to a genjutsu that lowers the attack. 

“Scratch one last time.” Naruto declares before Rubedo lunges, digging his talons into Kipper’s side before Kipper collapses. 

“What!?” May asks in disbelief. Naruto calls Rubedo back to him before spraying one of the potions on his bruised shoulder. 

“That was a pretty good try, May.” May blushes, obviously thoroughly embarrassed at being beaten by him. 

“Yeah, you were pretty good too. How many trainers have you battled to get Rubedo that tough?” Naruto blinks at her, astounded at her question. 

“I’ve been training against wild pokemon.” She stares at him, and he realizes that she doesn’t believe him. He pulls out his trainer card, which has now registered her as his first win before he shows it to her. She whistles sharply. 

“You must be a Drill Sergeant.” She shudders a little at the thought. 

Naruto laughs, “No, if you want a Drill Sergeant go meet Tsunade.” May pales at the thought there is someone tougher than him and Naruto comes over to her mudkip, a little disappointed that she isn’t tending to him. 

“Oh, Kipper…” May comes over to him and Naruto helps her return him to the pokeball before she smiles at him. “Professor Birch is waiting for you in Littleroot town. I’ve gotta go train Kipper and get a balanced team ready for our next fight against you.” Naruto chuckles, remembering that there are wingull on this route. 

“I’m going to go meet with him, do you need an escort back to the closest town?” she shakes her head. 

“I’ll be fine, I'll revive my Kipper and continue using the Revive I bought.” She pulls out a medicine and Naruto watches as Kipper wakes up. Then he carefully uses his potion on Kipper’s wounds.

Kipper stays quiet, now peering at him, he is curious of all things. “I’ll be going now.” Naruto turns and heads back toward Oldale town to rest with Rubedo at the Pokemon Center. Then he is off towards Littleroot Town.

* * *

Arriving in the pokemon lab Naruto makes his way up to Professor Birch and smiles at him. “I heard that you beat May on your first try. She happened to beat my son on her first try and he is experienced so I wasn’t sure if you would win or not.” Rubedo squawks a little at being questioned. “There’s the little victor!” Rubedo blushes again before squawking as professor birch lifts him onto the table. He observes him for several moments. 

“Is something wrong?” Naruto asks him. 

Birch looks at him with a bright smile. “Of course not, I was checking to see if I am imagining it but your Rubedo is better than he was last week when I gave him to you. He looks more buffed up and he is very happy.” Rubedo trills in agreement and Naruto chuckles.

“Yeah, I know May called me a Drill Sergeant but I really did work him hard during the last week.” Birch nods to him before he smiles. 

“Looks like it is time for you to head toward Roxanne. You have a ways to go but I believe in you. I know you will win against her on your first try! According to May you beat Mudkip in three hits. Usually it takes about nine hits for the average pokemon to defeat a pokemon of a near equal level unless support moves are mostly used by one or the other.” Naruto blushes, knowing that he is being praised by the man. 

“Thanks, I reckon that I might need to actually use some pokeballs to get some support pokemon. I really want a Zigzagoon. They pick up and find random things so they are certainly useful. Maybe even going as far as to get three of them in my main party.” 

“That’s a fine idea. Why don’t you go ahead and try to take on the Gyms and then the elite four. You might even become the champion at the rate of progress that you are having!” Naruto blushes again as he scoops Rubedo up to head toward the door. 

“You’re embarrassing me. I’m gone for now.” Birch chuckles as he heads out of the lab. Seeing nothing that he wants to explore he heads toward Oldale town and decides to head west.

* * *


End file.
